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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ), 'gf_id' => 'HOM05D001290', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001290' ), 'data_identifier' => 'HOM05D001290', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001290', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '486', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p30750' => 'bna', 'A03p37580' => 'bna', 'A04p29490' => 'bna', 'A05p37070' => 'bna', 'A09p00390' => 'bna', 'Aa31LG3G15770' => 'aar', 'Aa31LG3G6520' => 'aar', 'Aa31LG5G23310' => 'aar', 'Aa31LG5G390' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.2380' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.392' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_369.288' => 'aag', 'Actinidia09999' => 'ach', 'Actinidia11469' => 'ach', 'Actinidia24330' => 'ach', 'Ah.05g176440' => 'amhyb', 'Ah.08g219530' => 'amhyb', 'Ah.12g055120' => 'amhyb', 'AL3G23950' => 'aly', 'AL4G35940' => 'aly', 'AL6G52820' => 'aly', 'AL6G52832' => 'aly', 'AL6G52834' => 'aly', 'Aqoxy5G00715' => 'aox', 'Aqoxy5G01491' => 'aox', 'Aqoxy7G04045' => 'aox', 'arahy.Tifrunner.gnm1.ann1.3KC6N2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.89FLHR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EFL7R6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IQ0HIS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KV7TM3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.M7AR10' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TBV1EQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UDM5UK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YZ2FZM' => 'arhy', 'AT2G38660' => 'ath', 'AT3G12290' => 'ath', 'AT4G00600' => 'ath', 'AT4G00620' => 'ath', 'ATR0100G005' => 'atr', 'ATR0100G016' => 'atr', 'ATR0745G012' => 'atr', 'ATR0796G026' => 'atr', 'ATR0796G157' => 'atr', 'ATR0796G213' => 'atr', 'ATR1127G051' => 'atr', 'Atru.BG.174.p' => 'acertr', 'Atru.chr12.1492' => 'acertr', 'Atru.chr4.2080' => 'acertr', 'Atru.chr5.1199' => 'acertr', 'Atru.chr5.448' => 'acertr', 'Atru.chr8.18' => 'acertr', 'AUR62001783' => 'cqu', 'AUR62001786' => 'cqu', 'AUR62004318' => 'cqu', 'AUR62007297' => 'cqu', 'AUR62009571' => 'cqu', 'AUR62009575' => 'cqu', 'AUR62018708' => 'cqu', 'AUR62023439' => 'cqu', 'AUR62033326' => 'cqu', 'AUR62033333' => 'cqu', 'AUR62035409' => 'cqu', 'AUR62035410' => 'cqu', 'AUR62035697' => 'cqu', 'BcaB01g00282' => 'bca', 'BcaB01g02262' => 'bca', 'BcaB01g02485' => 'bca', 'BcaB01g03667' => 'bca', 'BcaB02g11548' => 'bca', 'BcaB03g13489' => 'bca', 'BcaB04g18686' => 'bca', 'BcaB04g21087' => 'bca', 'BcaC01g04054' => 'bca', 'BcaC02g07454' => 'bca', 'BcaC04g24157' => 'bca', 'BcaC05g29271' => 'bca', 'BcaC06g36493' => 'bca', 'BcaC06g36497' => 'bca', 'BcaNung07164' => 'bca', 'BolC3t16037H' => 'bol', 'BolC3t16834H' => 'bol', 'BolC4t28182H' => 'bol', 'BolC5t34216H' => 'bol', 'BolC7t40757H' => 'bol', 'BolC7t40761H' => 'bol', 'BolC8t46807H' => 'bol', 'BolC8t50476H' => 'bol', 'BolC9t52985H' => 'bol', 'BraA03t12254Z' => 'bra', 'BraA03t12912Z' => 'bra', 'BraA04t18416Z' => 'bra', 'BraA05t22504Z' => 'bra', 'BraA09t35722Z' => 'bra', 'C03p37450' => 'bna', 'C03p45570' => 'bna', 'C04p66810' => 'bna', 'C05p55500' => 'bna', 'C07p03610' => 'bna', 'C07p03640' => 'bna', 'C08p00080' => 'bna', 'C08p28720' => 'bna', 'C09p00510' => 'bna', 'CAN.G110.9' => 'can', 'CAN.G128.89' => 'can', 'CAN.G78.30' => 'can', 'CANSAT21G2623' => 'cansat', 'CANSAT25G2526' => 'cansat', 'CANSAT56G2667' => 'cansat', 'CARHR086840' => 'chi', 'CARHR133330' => 'chi', 'CARHR248240' => 'chi', 'CARHR248770' => 'chi', 'CARHR289600' => 'chi', 'Carub.0003s1166' => 'cru', 'Carub.0004s2064' => 'cru', 'Carub.0006s3631' => 'cru', 'Carub.0006s3657' => 'cru', 'Carub.0006s3658' => 'cru', 'Carub.0006s3659' => 'cru', 'Carub.0006s3660' => 'cru', 'Carub.0006s3661' => 'cru', 'Ca_07889_v3' => 'car', 'Ca_09144_v3' => 'car', 'Ca_12610_v3' => 'car', 'Ca_14033_v3' => 'car', 'Ca_14081_v3' => 'car', 'Ca_14252_v3' => 'car', 'CBR_g23792' => 'cbr', 'CBR_g3728' => 'cbr', 'Cc01_g06410' => 'ccan', 'Cc01_g20610' => 'ccan', 'Cc02_g37610' => 'ccan', 'Cc02_g37630' => 'ccan', 'Cc07_g13410' => 'ccan', 'CDE09G0154' => 'cde', 'CDE10G0330' => 'cde', 'CDE12G0234' => 'cde', 'CDE12G0449' => 'cde', 'Cfa005956' => 'cfa', 'Cfa016977' => 'cfa', 'Ciclev10012007m.g' => 'ccl', 'Ciclev10020642m.g' => 'ccl', 'Ciclev10021378m.g' => 'ccl', 'CiPaw.01G057700' => 'cil', 'CiPaw.01G162400' => 'cil', 'CiPaw.08G097600' => 'cil', 'CiPaw.10G167600' => 'cil', 'ClCG04G005110' => 'cla', 'ClCG05G001710' => 'cla', 'ClCG10G010760' => 'cla', 'COL.COLO4_02435' => 'col', 'COL.COLO4_07713' => 'col', 'COL.COLO4_12674' => 'col', 'COL.COLO4_23386' => 'col', 'Cpa.g.sc0.4' => 'cpa', 'Cpa.g.sc169.41' => 'cpa', 'Cpa.g.sc18.223' => 'cpa', 'Cre03.g162650' => 'cre', 'Cre03.g182450' => 'cre', 'Cre17.g698450' => 'cre', 'CsaV3_3G009100' => 'csa', 'CsaV3_4G000560' => 'csa', 'CsaV3_4G013530' => 'csa', 'CSS0012762' => 'camsi', 'CSS0023169' => 'camsi', 'CSS0026095' => 'camsi', 'CSS0042162' => 'camsi', 'DCAR_005808' => 'dca', 'DCAR_015946' => 'dca', 'DCAR_025144' => 'dca', 'DCAR_031738' => 'dca', 'Dinv19721' => 'din', 'Dinv22439' => 'din', 'Dinv25384' => 'din', 'Dinv32448' => 'din', 'Dinv33032' => 'din', 'Dinv43782' => 'din', 'Dinv43784' => 'din', 'Duzib138G1426' => 'dzi', 'Duzib151G0026' => 'dzi', 'ECA236G0180' => 'eca', 'ECA238G4538' => 'eca', 'ECA247G0973' => 'eca', 'ECA248G1693' => 'eca', 'EL10Ac1g00527' => 'bvu', 'EL10Ac1g02237' => 'bvu', 'EL10Ac2g02394' => 'bvu', 'EL10Ac7g16021' => 'bvu', 'Eucgr.E00181' => 'egr', 'Eucgr.E00183' => 'egr', 'Eucgr.E03447' => 'egr', 'Eucgr.J01710' => 'egr', 'Eucgr.J01713' => 'egr', 'Eucgr.J01714' => 'egr', 'Eucgr.J01717' => 'egr', 'Eucgr.K01319' => 'egr', 'Eucgr.K03460' => 'egr', 'FAN03G2178' => 'fan', 'FAN05G4073' => 'fan', 'FAN06G3059' => 'fan', 'FAN06G4760' => 'fan', 'FAN09G1204' => 'fan', 'FAN10G0069' => 'fan', 'FAN14G1833' => 'fan', 'FAN15G3691' => 'fan', 'FAN20G2277' => 'fan', 'FAN23G1540' => 'fan', 'FAN24G1107' => 'fan', 'FAN27G1146' => 'fan', 'FAN28G0677' => 'fan', 'FvH4_1g00020' => 'fve', 'FvH4_2g25270' => 'fve', 'FvH4_6g09070' => 'fve', 'FvH4_7g13650' => 'fve', 'Glyma.03G000600' => 'gma', 'Glyma.03G212700' => 'gma', 'Glyma.06G315600' => 'gma', 'Glyma.06G316100' => 'gma', 'Glyma.09G262300' => 'gma', 'Glyma.18G229900' => 'gma', 'Glyma.19G209700' => 'gma', 'Gohir.A07G120500' => 'ghi', 'Gohir.A10G197300' => 'ghi', 'Gohir.A12G010400' => 'ghi', 'Gohir.D07G124700' => 'ghi', 'Gohir.D10G204150' => 'ghi', 'Gohir.D10G204401' => 'ghi', 'Gohir.D12G010600' => 'ghi', 'Gorai.001G134500' => 'gra', 'Gorai.008G010500' => 'gra', 'Gorai.011G229100' => 'gra', 'Gorai.011G229400' => 'gra', 'GSVIVG01026845001' => 'vvi', 'GSVIVG01027968001' => 'vvi', 'GSVIVG01029826001' => 'vvi', 'HanXRQChr01g0000651' => 'han', 'HanXRQChr04g0121621' => 'han', 'HanXRQChr10g0284491' => 'han', 'HanXRQChr15g0483701' => 'han', 'Haze_00941' => 'cav', 'Haze_04886' => 'cav', 'Haze_21231' => 'cav', 'Haze_27398' => 'cav', 'Hma1.2p1_0033F.1_g020390' => 'hma', 'Hma1.2p1_0169F.1_g074880' => 'hma', 'Hma1.2p1_0209F.1_g088660' => 'hma', 'HPP92_024327' => 'vpl', 'HPP92_024775' => 'vpl', 'HPP92_024776' => 'vpl', 'Hund04957' => 'sun', 'Hund05231' => 'sun', 'Hund11234' => 'sun', 'Hund14557' => 'sun', 'Hund16941' => 'sun', 'Hund27302' => 'sun', 'Lalb_Chr04g0256731' => 'lal', 'Lalb_Chr13g0290281' => 'lal', 'Lalb_Chr15g0078591' => 'lal', 'Lj1A346T33' => 'lonja', 'Lj1C0T4' => 'lonja', 'Lj1C33T2' => 'lonja', 'Lj1g0012337' => 'lja', 'Lj1g0016182' => 'lja', 'Lj1g0025280' => 'lja', 'Lj1g0025392' => 'lja', 'Lj2A1190G60' => 'lonja', 'Lj2A53G25' => 'lonja', 'Lj3g0007310' => 'lja', 'Lj3g0013292' => 'lja', 'Lj4g0019550' => 'lja', 'Lj9A580T59' => 'lonja', 'Lsat_1_v5_gn_2_63561' => 'lsa', 'Lsat_1_v5_gn_3_43481' => 'lsa', 'Lsat_1_v5_gn_4_163640' => 'lsa', 'Lsat_1_v5_gn_5_153480' => 'lsa', 'Lsat_1_v5_gn_7_5121' => 'lsa', 'Lsat_1_v5_gn_9_51801' => 'lsa', 'Manes.01G216600' => 'mes', 'Manes.04G151700' => 'mes', 'Manes.05G064400' => 'mes', 'Manes.09G119500' => 'mes', 'Mapoly0012s0185' => 'mpo', 'Mapoly0040s0061' => 'mpo', 'Mapoly0060s0017' => 'mpo', 'MBI03_g00293_MAGBIO' => 'mbi', 'MBI04_g00380_MAGBIO' => 'mbi', 'MBI04_g07000_MAGBIO' => 'mbi', 'MBI18_g11417_MAGBIO' => 'mbi', 'MCO01G411' => 'mco', 'MCO07G477' => 'mco', 'MCO11G603' => 'mco', 'MD03G1140500' => 'mdo', 'MD03G1284400' => 'mdo', 'MD03G1284500' => 'mdo', 'MD04G1172600' => 'mdo', 'MD04G1181400' => 'mdo', 'MD07G1141500' => 'mdo', 'MD08G1243500' => 'mdo', 'MD11G1025400' => 'mdo', 'MD11G1304100' => 'mdo', 'MD15G1270000' => 'mdo', 'MD16G1138100' => 'mdo', 'Medtr1g030450' => 'mtr', 'Medtr3g007490' => 'mtr', 'Medtr3g007580' => 'mtr', 'Medtr3g007620' => 'mtr', 'Medtr7g076680' => 'mtr', 'Medtr7g108580' => 'mtr', 'MELO3C006130.2' => 'cme', 'MELO3C017979.2' => 'cme', 'MELO3C025279.2' => 'cme', 'Migut.B01723' => 'egut', 'Migut.J00003' => 'egut', 'Migut.N01497' => 'egut', 'MSTRG.17250' => 'ama', 'MSTRG.17416' => 'ama', 'MSTRG.5475' => 'ama', 'Nitab4.5_0000075g0070' => 'nta', 'Nitab4.5_0000524g0090' => 'nta', 'Nitab4.5_0000890g0050' => 'nta', 'Nitab4.5_0001251g0030' => 'nta', 'Nitab4.5_0002606g0040' => 'nta', 'Nitab4.5_0002606g0050' => 'nta', 'Nitab4.5_0003111g0090' => 'nta', 'Nitab4.5_0006089g0040' => 'nta', 'Nitab4.5_0006963g0010' => 'nta', 'Nitab4.5_0011810g0020' => 'nta', 'Nitab4.5_0017610g0010' => 'nta', 'Nn5g26731' => 'nnu', 'Nn5g28273' => 'nnu', 'Nn5g30729' => 'nnu', 'Oeu014676.1' => 'oeu', 'Oeu026907.3' => 'oeu', 'Oeu046694.1' => 'oeu', 'Oeu056347.1' => 'oeu', 'Oeu058086.1' => 'oeu', 'Os02g0120900' => 'osa', 'Os05g0150800' => 'osa', 'Os09g0327300' => 'osa', 'Peaxi162Scf00047g00731' => 'pax', 'Peaxi162Scf00397g00016' => 'pax', 'Peaxi162Scf00427g00718' => 'pax', 'Peaxi162Scf00673g00448' => 'pax', 'Peaxi162Scf01181g00013' => 'pax', 'Peaxi162Scf01944g00014' => 'pax', 'Peaxi162Scf03024g00008' => 'pax', 'PGR004G2224' => 'pgr', 'PGR042G0733' => 'pgr', 'PGR119G0223' => 'pgr', 'PGSC0003DMG400000152' => 'stu', 'PGSC0003DMG400017702' => 'stu', 'PGSC0003DMG401028101' => 'stu', 'PGSC0003DMG402028101' => 'stu', 'Phvul.001G205500' => 'pvu', 'Phvul.008G068000' => 'pvu', 'Phvul.010G060500' => 'pvu', 'Potri.002G157100' => 'ptr', 'Potri.006G114100' => 'ptr', 'Potri.011G098600' => 'ptr', 'Potri.014G080701' => 'ptr', 'Pp3c11_24200' => 'ppa', 'Pp3c22_13130' => 'ppa', 'Pp3c27_5410' => 'ppa', 'Pp3c6_29520' => 'ppa', 'Pp3c7_11840' => 'ppa', 'Pp3c7_1350' => 'ppa', 'Prupe.1G144700' => 'ppe', 'Prupe.2G162600' => 'ppe', 'Prupe.6G126200' => 'ppe', 'Prupe.6G300800' => 'ppe', 'Prupe.8G257500' => 'ppe', 'Psat3g022680' => 'psa', 'Psat3g110960' => 'psa', 'Psat5g229680' => 'psa', 'Psat6g042160' => 'psa', 'PSO210G2074' => 'pso', 'PSO210G3638' => 'pso', 'PSO339G3846' => 'pso', 'PSO339G4100' => 'pso', 'PSO339G5636' => 'pso', 'PSO339G5705' => 'pso', 'PSO384G0407' => 'pso', 'PSO384G0601' => 'pso', 'PSO384G1295' => 'pso', 'PSO384G1573' => 'pso', 'PSO384G3647' => 'pso', 'PSO384G4614' => 'pso', 'PSO675G2198' => 'pso', 'PSO832G2539' => 'pso', 'QL06p003664' => 'qlo', 'QL06p003666' => 'qlo', 'QL07p030215' => 'qlo', 'QL07p030218' => 'qlo', 'QL07p034283' => 'qlo', 'QL08p049556' => 'qlo', 'QL12p027075' => 'qlo', 'RcHm_v2.0_Chr1g0353731' => 'rch', 'RcHm_v2.0_Chr2g0084241' => 'rch', 'RcHm_v2.0_Chr3g0459301' => 'rch', 'RcHm_v2.0_Chr3g0495451' => 'rch', 'RcHm_v2.0_Chr6g0293401' => 'rch', 'Rhsim01G0283500' => 'rsi', 'Rhsim02G0054100' => 'rsi', 'Rhsim09G0000600' => 'rsi', 'Rhsim09G0038800' => 'rsi', 'RhsimUnG0002200' => 'rsi', 'Sabra02G0124700' => 'sbr', 'Sabra06G0089000' => 'sbr', 'Sabra11G0084200' => 'sbr', 'Sabra11G0085400' => 'sbr', 'SalBow1G0616' => 'sbo', 'SalBow1G7670' => 'sbo', 'SalBow1G8177' => 'sbo', 'SalBow1G8280' => 'sbo', 'SalBow2G1323' => 'sbo', 'SalBow3G4521' => 'sbo', 'Sc06g0008320' => 'sci', 'Sc12g0004270' => 'sci', 'Sc22g0001510' => 'sci', 'Sc23g0003070' => 'sci', 'Sc23g0003080' => 'sci', 'Sed0006146' => 'sed', 'Sed0006905' => 'sed', 'Sed0018979' => 'sed', 'SEGI_00035' => 'sgi', 'SEGI_09851' => 'sgi', 'SEGI_17096' => 'sgi', 'SEGI_21326' => 'sgi', 'SEGI_24015' => 'sgi', 'SEGI_36500' => 'sgi', 'SEGI_40730' => 'sgi', 'SGA_v2.0_scaffold135G34946' => 'sas', 'SGA_v2.0_scaffold277G46675' => 'sas', 'SGA_v2.0_scaffold297G47603' => 'sas', 'SGA_v2.0_scaffold85G26584' => 'sas', 'SGA_v2.0_scaffold95G28854' => 'sas', 'SMO145G0225' => 'smo', 'SMO196G0034' => 'smo', 'SMO334G0070' => 'smo', 'Solyc01g094280.3' => 'sly', 'Solyc08g048240.4' => 'sly', 'Solyc10g080970.2' => 'sly', 'Sopen01g038080' => 'spe', 'Sopen08g015350' => 'spe', 'Sopen10g031480' => 'spe', 'Sp3g10510' => 'spa', 'Sp4g21000' => 'spa', 'Sp6g00640' => 'spa', 'TAR369G0331' => 'tar', 'TAR376G0927' => 'tar', 'TAR628G0062' => 'tar', 'TAR636G3000' => 'tar', 'THA.LOC104805878' => 'tha', 'THA.LOC104806321' => 'tha', 'THA.LOC104826751' => 'tha', 'Thecc.01G296200' => 'tca', 'Thecc.01G363400' => 'tca', 'Thecc.04G061500' => 'tca', 'Thhalv10016863m.g' => 'esa', 'Thhalv10021228m.g' => 'esa', 'Thhalv10028771m.g' => 'esa', 'Thhalv10029292m.g' => 'esa', 'TPR.G25524' => 'tpr', 'TPR.G25819' => 'tpr', 'TPR.G33554' => 'tpr', 'TPR.G36038' => 'tpr', 'TPR.G40183' => 'tpr', 'TPR.G9621' => 'tpr', 'TWI14G0598' => 'twi', 'TWI23G0242' => 'twi', 'TWI74G0771' => 'twi', 'unitig_0.g1005' => 'ugi', 'unitig_0.g1276' => 'ugi', 'unitig_0.g1277' => 'ugi', 'unitig_22.g6623' => 'ugi', 'vmacro14993' => 'vma', 'vmacro20956' => 'vma', 'vmacro21101' => 'vma', 'VMungo0331G0026' => 'vmu', 'VMungo0331G0063' => 'vmu', 'VMungo1383G1521' => 'vmu', 'VMungo1383G2573' => 'vmu', 'Zm00001eb098250' => 'zma', 'Zm00001eb208240' => 'zma', 'Zm00001eb354230' => 'zma' ) $gf_id = 'HOM05D001290' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001290' ) $data_identifier = 'HOM05D001290' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 14, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 5, 'aox' => (int) 3, 'arhy' => (int) 9, 'ath' => (int) 4, 'atr' => (int) 7, 'acertr' => (int) 6, 'cqu' => (int) 13, 'bca' => (int) 15, 'bol' => (int) 9, 'bra' => (int) 5, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 5, 'cru' => (int) 8, 'car' => (int) 6, 'cbr' => (int) 2, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 9, 'fan' => (int) 13, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 7, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 4, 'cav' => (int) 4, 'hma' => (int) 3, 'vpl' => (int) 3, 'sun' => (int) 6, 'lal' => (int) 3, 'lonja' => (int) 6, 'lja' => (int) 7, 'lsa' => (int) 6, 'mes' => (int) 4, 'mpo' => (int) 3, 'mbi' => (int) 4, 'mco' => (int) 3, 'mdo' => (int) 11, 'mtr' => (int) 6, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 3, 'nta' => (int) 11, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 6, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 14, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 5, 'sbr' => (int) 4, 'sbo' => (int) 6, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb354230' $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